Make sure that you have fitted the correct Smart Pie controller into the Smart Pie
(they might look the same, but they are actually different). The MP4 controller is usually marked 25 Amps and the Smart Pie controller is usually marked 18 Amps.
There have been several reports of this intermittent pedelec assistance, but unfortunately I don't recall seeing a solution to it. I suggest you contact your supplier and see if they can offer advice. If they are unable to help then you will have to contact David at Golden Motor in China.
If the magnet ring maintains a constant gap with the sensor as the pedals are rotated then it is unlikely to be a sensor problem, although it might just be worth checking the polarity of the five magnets to ensure they are
all fitted with the same magnetic orientation.
(You can use another magnet to check the magnetic polarity.)It is worth checking for excessive play in the Bottom Bracket, as this could also cause variation in the gap between the magnet ring and the sensor.
Some Smart Pies have a slight amount of rotational movement between the stator/controller housing and the axle which can produce a clonk as the movement is taken up when power is applied or regen in operated, and if this is the cause, reducing the "Acceleration" setting should improve this clonk.
If the new controller is constantly noisy under even load, perhaps it is actually an older
(non-vector) controller.
Alan